One class support vector machine for predicting avian-to-human transmission of avian influenza A virus

Avian influenza A virus (AIV) can cross the host barrier to infect human directly and has continuously been reported to cause human death worldwide. Predicting which AIVs can directly transmit from avian to human will provide early warning of AIVs with human pandemic potential, which is beneficial to public health. Although it is easy to decide a dataset of AIVs having the capability of avian-to-human transmission as positive samples, there are no experimentally confirmed AIVs without the capability to be considered as negative samples. Therefore, in this study we utilized one-class support vector machines (OCSVM) to solve this one-class classification problem. With two feature sets including amino acid composition and Moran autocorrelation, an OCSVM-based prediction model was constructed and demonstrated to achieve good performances on both the training dataset and the external testing dataset. The experimental results imply that the model constructed on only positive samples (AIVs having the capability of avian-to-human transmission) is efficient to predict avian-to-human transmission of AIVs.

[1]  Bernhard Schölkopf,et al.  Estimating the Support of a High-Dimensional Distribution , 2001, Neural Computation.

[2]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[3]  M. Peiris,et al.  Human infection with influenza H9N2 , 1999, The Lancet.

[4]  Y. Guan,et al.  Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia , 2004, Nature.

[5]  Wei-Gang Hu,et al.  Correlated mutations in the four influenza proteins essential for viral RNA synthesis, host adaptation, and virulence: NP, PA, PB1, and PB2 , 2010 .

[6]  D. J. Stevens,et al.  The Structure and Receptor Binding Properties of the 1918 Influenza Hemagglutinin , 2004, Science.

[7]  B. Murphy,et al.  A single amino acid in the PB2 gene of influenza A virus is a determinant of host range , 1993, Journal of virology.

[8]  Christopher N. Larsen,et al.  BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulence , 2007, Nucleic Acids Res..

[9]  C. Naeve,et al.  Mutations in the hemagglutinin receptor-binding site can change the biological properties of an influenza virus , 1984, Journal of virology.

[10]  Minoru Kanehisa,et al.  AAindex: amino acid index database, progress report 2008 , 2007, Nucleic Acids Res..

[11]  Zheng Kou,et al.  Prediction of interspecies transmission for avian influenza A virus based on a back-propagation neural network , 2010, Math. Comput. Model..

[12]  H. Klenk,et al.  Molecular mechanisms of interspecies transmission and pathogenicity of influenza viruses: Lessons from the 2009 pandemic , 2011, BioEssays : news and reviews in molecular, cellular and developmental biology.

[13]  Yukiko Muramoto,et al.  Pathogenicity of highly pathogenic avian H5N1 influenza A viruses isolated from humans between 2003 and 2008 in northern Vietnam , 2010, The Journal of general virology.

[14]  T. Tatusova,et al.  The Influenza Virus Resource at the National Center for Biotechnology Information , 2007, Journal of Virology.

[15]  Marion Koopmans,et al.  Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[16]  S. Cusack,et al.  Host Determinant Residue Lysine 627 Lies on the Surface of a Discrete, Folded Domain of Influenza Virus Polymerase PB2 Subunit , 2008, PLoS pathogens.

[17]  Chih-Jen Lin,et al.  LIBSVM: A library for support vector machines , 2011, TIST.

[18]  Y. Guan,et al.  Establishment of multiple sublineages of H5N1 influenza virus in Asia: implications for pandemic control. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Zejun Li,et al.  Identification of Amino Acids in HA and PB2 Critical for the Transmission of H5N1 Avian Influenza Viruses in a Mammalian Host , 2009, PLoS pathogens.

[20]  Yi Guan,et al.  Full Factorial Analysis of Mammalian and Avian Influenza Polymerase Subunits Suggests a Role of an Efficient Polymerase for Virus Adaptation , 2009, PloS one.

[21]  Kwok-Hung Chan,et al.  Infection of immunocompromised patients by avian H9N2 influenza A virus. , 2011, The Journal of infection.

[22]  X M Pan,et al.  Accurate Prediction of Protein Secondary Structural Content , 2001, Journal of protein chemistry.

[23]  D. Horne,et al.  Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities , 1988, Biopolymers.

[24]  N. Cox,et al.  Characterization of an avian influenza A (H5N1) virus isolated from a child with a fatal respiratory illness. , 1998, Science.

[25]  Martin Hirst,et al.  Human Illness from Avian Influenza H7N3, British Columbia , 2004, Emerging infectious diseases.

[26]  David J. Stevens,et al.  Haemagglutinin mutations responsible for the binding of H5N1 influenza A viruses to human-type receptors , 2006, Nature.

[27]  H. Yassine,et al.  Interspecies and intraspecies transmission of influenza A viruses: viral, host and environmental factors , 2010, Animal Health Research Reviews.